In a study of the crystal structure of calcium/calmodulin dependent protein kinase, a subdomain of the kinase was expressed in a cultured cell line. However, the expressed protein did not form useful crystals for X-ray crystallography. The SDS-gel analysis results showed that the expressed protein was in a truncated form. To determine where the protein was truncated, matrix-assisted laser desorption mass spectrometry was used. In the first step of this study, we measured the molecular weight of the expressed protein kinase subdomain. The mass spectrometric analysis results showed that two major forms existed. One of them is truncated at the histidine tail, added for separation purposes. The other component is a longer form, produced by failure of termination of translation at the chain-terminating codon. Based on this finding, a new expression system was designed and constructed, leading to a successful X-ray structure of the protein. Mass spectrometric measurements were carried out on grpE and dnak proteins after treatment with enzymes, giving an indication of the minimum domain required for complex formation and facilitating x-ray crystallographic structure analysis.